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H5N1, H7N9 and beyond: FAO investigates avian influenza virus diversity, geographical spread and risks at the human-animal interface

17 March 2015 - Over the past two years, the world has witnessed an increase in emergence of novel avian influenza (AI) subtypes, such as H5N2, H5N6, H5N8, H7N9, H10N8 – to name the few making headlines. AI is a disease of poultry, able to incur devastating losses to the poultry industry and threaten poultry-dependent livelihoods. Some AI viruses are zoonotic and can infect humans, sometimes causing severe disease and death. It is feared that such viruses could gain the potential to transmit easily between humans and lead to a pandemic. Adaptation of AI viruses is made possible by their constantly changing genome, either through mutation of genes (called ‘genetic drift’) or exchange of genes from other influenza viruses (‘genetic shift’ or ‘reassortment’). These genetic changes may modify biological properties of the virus, e.g. enhance pathogenicity for poultry or increase transmission to humans. In this way H5N2, H5N6 and H5N8 viruses derived through reassortment from zoonotic highly pathogenic avian influenza (HPAI) H5N1 that since 2003 has been causing huge losses to the poultry industry in countries worldwide and over 780 human cases with 55 % human fatalities. Sporadic human infections with H5N6 and H10N8 avian viruses have also been reported. Another novel reassortant virus, H7N9, already caused over 600 human cases in the past two years, almost 40 % of which have died. This virus is low pathogenic in poultry and not leading to any disease signs, which makes it extremely difficult to detect in poultry populations.

As part of pandemic preparedness and for early warning purposes, it is of utmost importance to closely monitor the AI virus gene pool worldwide. To do so FAO has implemented several projects and provides guidance, coordination and tools to its member countries in the following areas:


For a decade FAO has been supporting AI surveillance in member countries worldwide. Following the emergence and spread of HPAI H5N1 in 2004, more than 200 projects have been implemented since, both in affected countries and regions and in countries at risk. FAO’s portfolio spans (i) early detection of virus incursion, (ii) monitoring of endemic situations and viral gene pools, (iii) identification of risk factors for emergence and spread, (iv) risk assessment and (iv) risk mitigation. When avian influenza H7N9 emerged early 2013 in China, FAO called upon these mechanisms already in place to increase preparedness of countries for this previously unknown threat. Risk-based surveillance was implemented with countries assessed to be at risk of H7N9 incursion in Asia and Africa. The recent increase of AI virus diversity has led FAO to expand its surveillance approaches. In 2015 FAO started assisting both affected and at-risk countries with a more comprehensive AI surveillance strategy, actively searching for a wide array of virus sub-types and further characterizing those of interest.

Risk mitigation

FAO is also assisting countries to conduct value chain studies, mapping the poultry flow and identifying risk factors along the production chain. This work is crucial for the risk-based selection of surveillance sites and for targeting interventions aimed at reducing virus introduction or spread. In the framework of zoonotic diseases, like AI, FAO fosters national, regional and global networking as well as cross-sectoral collaboration between animal health and public health services for enhanced sharing of disease information and exchange of expertise.

Monitoring of virus diversity

FAO is consolidating the information generated through extensive surveillance networks and combines this data for analysis with environmental, socio-economic and genetic data. Such analysis is facilitated by the FAO Global Animal Disease Information System (EMPRES-i), a web-based platform for the collection, storage, analysis and sharing of information from multiple sources, such as FAO projects and reports, official governments, the World Animal Health Information Database (WAHID) of the World Organisation for Animal Health (OIE) and other technical partner institutions. One of its features, the Genetic Module, links EMPRES-i disease events with sequence information held in an influenza sequence database developed and maintained by the FAO Reference Centre in Bioinformatics, Switzerland. This enables integration of genetic data into epidemiological analysis while attaching accurate epidemiological information to virus sequences. Global analysis of virus diversity and monitoring of dominant influenza genes can so be combined with environmental and climatic data, wild bird migration routes, trade routes, vaccination coverage, etc, allowing for early identification of AI reassortants with pandemic potential and planning of surveillance in geographic areas that are most likely to produce or amplify such viruses. Working in close collaboration with OIE, the World Health Organization (WHO) and other partners, such as Reference Centres involved in AI research, FAO is contributing this data to the global efforts for pandemic preparedness.

Joining efforts

FAO is calling upon member countries to (i) pursue AI virus characterization beyond the H5 and H7 subtyping required by the OIE, (ii) apply whole genome sequencing of AI viruses, (iii) share sequence information in the public domain and (iv) facilitate the linking of epidemiological and virus data by providing month and year of isolation, species and district or province name when submitting sequences to public databases. These efforts will help protecting people’s lives and livelihoods.


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Poultry outbreaks or human infections caused by avian influenza viruses since 1 January 2013, by virus subtype


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